PEtab-GUI: a graphical user interface to create, edit, and inspect PEtab parameter estimation problems.
Where this comes from
- Record sourced from PubMed, PMID 41787963.
- Also identified by DOI 10.1093/bioinformatics/btag106 and PMC identifier 13012594.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
Parameter estimation is a cornerstone of data-driven modeling in systems biology. Yet, constructing such problems in a reproducible and accessible manner remains challenging. The PEtab format has established itself as a powerful community standard to encode parameter estimation problems, promoting interoperability and reusability. However, its reliance on multiple interlinked files-often edited manually-can introduce inconsistencies, and new users often struggle to navigate them. Here, we present PEtab-GUI, an open-source Python application designed to streamline the creation, editing, and validation of PEtab problems through an intuitive graphical user interface. PEtab-GUI integrates all PEtab components, including SBML models and tabular files, into a single environment with live error checking and customizable defaults. Interactive visualization and simulation capabilities enable users to inspect the relationship between the model and the data. PEtab-GUI lowers the barrier to entry for specifying standardized parameter estimation problems, making dynamic modeling more accessible, especially in educational and interdisciplinary settings. PEtab-GUI is implemented in Python, open-source under a 3-Clause BSD license. The code, designed to be modular and extensible, is hosted on https://github.com/PEtab-dev/PEtab-GUI, available as a Zenodo repository at https://doi.org/10.5281/zenodo.15355752, and can be installed from PyPI.
Medical subject headings
- User-Computer Interface
- Software
- Computer Graphics
- Systems Biology